Genetics and Molecular Bio Final

If guanine makes up 28% of the bases in a sample of DNA, then thymine would make up what percentage of the bases?

A) 15%

B) 22%

C) 28%

D) 30%

E) 40%

B) 22%

Which of the following statements about base pairing is FALSE?

A) The purine will base pair with pyrimidine

B) Base pairs form between DNA strands, between DNA and RNA, and between RNA strands

C) Base pairing is required for proper replication of DNA

D) Base pairing is based on hydrogen bonding

E) It takes more energy to break AT base pairs than GC base pairs

E) It takes more energy to break AT base pairs than GC base pairs

In a DNA replication fork, the primer 5’ AAUUCCGGUCG 3’ would be hybridized (annealed) to which DNA sequence?

A) 3’ TTAAGGCCAGC 5’

B) 5’ AATTCCGGTCG 3’

C) 5’ TTAAGGCCAGC 3’

A) 3’ TTAAGGCCAGC 5’

Which chemical group is at the 3’ end of a single polynucleotide strand?

A) Phosphate group

B) Hydroxyl group

C) Purine base

D) Nitrogen group

E) Methyl group

B) Hydroxyl group

Which of the following statements about DNA structure is FALSE?

A) DNA can form both right-handed and left-handed helices

B) Standard B-form DNA has a major and minor groove, with better access to the nitrogen bases in the major groove

C) The sugar-phosphate backbone is found in the middle of the DNA molecule and the bases face out

D) The individual monomers of DNA are nucleotides, and they consist of a sugar, phosphate, and a nitrogenous base.

E) Covalent phosphodiester bonds link together nucleotides on the same strand and hydrogen bonds hold the two strands of DNA together

C) The sugar-phosphate backbone is found in the middle of the DNA molecule and the bases face out

Which of the following statements about chromatin structure is FALSE?

A) Regions of chromosome that form heterochromatin are generally areas of very active gene expression

B) A nucleosome is composed of DNA wrapped around a core of histone proteins

C) Heterochromatin commonly contains methylated DNA

D) Euchromatin commonly contains acetylated histones

A) Regions of chromosome that form heterochromatin are generally areas of very active gene expression

DNA replication begins at _________, where _______ is created with two _______, one on each side.

A) origin of replication; a replication bubble; replication forks

B) A replication bubble; an origin of replication; replication forks

C) An origin of replication; a replication fork; replication bubbles

D) A replication fork; a replication bubble; origins of replication

A) origin of replication; a replication bubble; replication forks

Which of the following tasks is DNA Polymerase capable of?

* Adding a DNA nucleotide to teh 5’ end of an existing strand with the help of an opposing strand template
* Starting a new strand of DNA
* Connecting adjacent strands of DNA together
* Adding a DNA nucleotide to the 3’ end of an existing strand with the help of an opposing strand template
* Separating strands of DNA

* Adding a DNA nucleotide to the 3’ end of an existing strand with the help of an opposing strand template

During DNA Replication, the first nucleotide of a new strand is put in position by __________.

A) DNA Polymerase, and it is a DNA nucleotide

B) Primase, and it is an RNA nucleotide

C) DNA Ligase, and it is a DNA nucleotide

D) Primase, and it is a DNA nucleotide

E) DNA Polymerase, and it is an RNA nucleotide

B) Primase, and it is an RNA nucleotide

Which of the following statements about lagging strand synthesis is FALSE?

A) Lagging strand synthesis is in the 5’ à 3’ direction

B) Replication of the lagging strand happens in small fragments

C) The first fragment is the one closest to the replication fork, and building in fragments continues until the origin of replication is reached

D) DNA Ligase is used to connect the fragment on the lagging strand

C)  The first fragment is the one closest to the replication fork, and building in fragments continues until the origin of replication is reached

Proofreading during DNA replication is possible due to ________.

A) The 3’ à 5’ exonuclease capability of DNA Polymerase

B) The 5’ à 3’ direction rule for strand synthesis

C) The ability of DNA Ligase to recognize mismatched pairs

D) A and B

E) All of the above

D) A and B

Which of the following statements about telomerase is FALSE?

A) It uses and RNA strand as a template

B) It helps to lengthen the ends of chromosomes

C) It solves a problem with replicating linear chromosomes where they get shorter

D) It is used in every human cell

E) It helps to extend the number of times a cell can divide

It is used in every human cell

If you perform a PCR on a DNA template with the sequence 5’ AAGCCTGCGTAAGCT 3’ with the primer 5’ACGCA 3’ the first nucleotide added to the primer will be:

A) A

B) T

C) C

D) G

D) G

Put the following steps of a PCR cycle in the correct order:                             

i. 50-60 °C to anneal the primers to the template

ii. 95 °C to denature the DNA

iii. 72 °C to allow the polymerase to build new DNA

B) ii → i → iii

In a Sanger sequencing reaction, incorporation of ___________ (for example) will prevent the addition of further nucleotides by DNA polymerase, because ___________.

A) Deoxyadenoside triphosphate (dATP)/dATP does not have a 5’ phosphate

B) Deoxyadenosine triphsosphate (dATP)/dATP does not have a 3’ hydroxyl group

C)Dideoxyadenosine triphosphate (ddATP)/ddATP does not have a 5’ phosphate

D)Dideoxyadenosine triphosphate (ddATP)/ddATP does not have a 3’ hydroxyl group

E)  Deoxyadenosine triphosphate (dATP)/dATP does not have a sugar group

D) Dideoxyadenosine triphosphate (ddATP)/ddATP does not have a 3’ hydroxyl group

You are attempting to create a reference genome sequence for a prokaryote you are working with that has a single chromosome. Unfortunately, it is difficult to grow in the lab, so you only have a small amount of DNA to work from. You get your results back and after assembly you have two separate, non-overlapping sequences. Quality control tests prove that these are sequences from your prokaryotes and there was no contamination. What could explain these results?

A) All of your reads cannot be joined into a single contig because some do not overlap

B) You did not have enough DNA to work from

C) You did not have enough coverage

D) A and B

E) All of the above

E) All of the above

Euchromatin

loosely packed DNA actively being read to produce proteins

Heterochromatin

tightly packed DNA not being read

Chromosome condensation

when DNA is more tightly packed, the genes are less likely to be read to make proteins

Acetylation

when done to histone proteins, it loosens the DNA packing

Methylation

when done to histone proteins, tightens the DNA packing

Origin of replication

specific sites (sequences) where DNA replication starts

Replication bubble

expanding area of replicated DNA

Replication fork

site of active replication, two per replication bubble

DNA Polymerases

add nucleotides to the 3’ end of a DNA strand

DNA Helicase

unwinds double-stranded DNA, but overwinds the DNA in front of it; works with Topoisomerase which reduces strain

Topoisomerase

Reduces strand strain

Primase

builds short RNA strands called primers that DNA Polymerase can work from to build a DNA strand

Leading strand

the strand during DNA replication that has a continuous synthesis; it is synthesized towards the replication fork

Lagging strand

a strand during DNA Replication which is synthesized using a series of segments called Okazaki fragments; fragments closer to the origin of replication are built first. It is synthesized away from the replication fork

Single Stranded Binding Proteins (SSBPs)

prevent the lagging strand from folding in on itself and blocking replication

DNA Polymerase III

the main DNA polymerase that works in the 5’ → 3’ direction. It also has 3’ → 5’ exonuclease capabilities for proofreading

DNA Polymerase I

a specialized DNA polymerase that works 5’ → 3’ with 3’ →5’ exonuclease capabilities. It also has a 5’ → 3’ exonuclease for replacing RNA primers with DNA

Exonuclease

cuts nucleotides off end of nucleic acid strand

DNA Ligase

connects adjacent strands of DNA together to combine Okazaki fragments to form one continuous new strand

Telomeres

non-protein coding repetitive sequence found at the ends of chromosomes that act as a buffer to protect coding genes

Telomerase

a protein-RNA complex that maintains telomere length in gamete producing cells.

Polymerase Chain Reaction (PCR)

A process where DNA strands are split and separated with heat, primers are added to the target DNA, and a DNA Polymerase extends from a primer using the target DNA as a template. The process is repeated to make copies of DNA sequences

GC base pairs are ___ than AT pairs so they can anneal at__ temperatures.

Longer sequences anneal at ____ temperatures

stronger; higher; higher

Gel Electrophoresis

uses electricity to separate DNA molecules by size (number of nucleotides)

Dideoxynucleotides (ddNTPs)

prematurely stop strand synthesis in Sanger sequencing

Sanger sequencing

similar to PCR, but only one primer is used and no chain reaction occurs; it sequences 100s to 1000s of nucleotides by combining the original DNA sequence, dNTPS, fluorescently labelled ddNTPs, and fluorescently labelled oligonucleotides. The sequence is then determined with size separation using gel electrophoresis, using the labelled ddNTPs to determine the nucleotide sequence

Contig

continuous segment of sequence created through overlapping “reads” (sequences)

Coverage

Number of copies of genome sequenced, more is needed for new genome assembly

RNA Polymerase

separates the strands of a DNA molecule to build a new RNA molecule 5’ → 3’ that is complementary to one of the DNA strands

Promoter DNA Sequences

mark the beginning of genes

Rho-independent (intrinsic) termination

caused by a hairpin in RNA transcript

Rho-dependent termination

Uses Rho translocase to remove RNA polymerase and DNA from transcript

End modification

5’ Methyl G Cap, 3’ poly-A tail; facilitate export from nucleus protect from degradation, facilitate translation

Exons

Protein coding DNA segments (expressed; exit the nucleus)

Introns

non protein coding (intervening)

RNA splicing

remove introns, connect exons before exit from nucleus

Spliceosome

protein-RNA complex that carries out RNA splicing

Small nuclear ribonucleoproteins (snRNPs)

targets complex based on intron sequences

messenger RNA (mRNA)

is read in the 5’ → 3’ direction to build new proteins in the N-terminus to C-terminus directions

codons

set of 3 RNA nucleotides, corresponds to one amino acid

anticodon

found at the end of the tRNA in translation, and base pair with the mRNA codon

Ribosome

rrNA-protein complex where two subunits come together to initiate translation. It has three tRNA binding sites: A site with tRNA-amino acid, P site with tRNA polypeptide, and E site with empty tRNA exits

Polyribosomes (polysomes)

multiple ribosomes simultaneously translate the same mRNA

Open Reading Frames (ORFs)

contain a start codon and no premature stop codons; help predict gene locations, especially in prokaryotes

Substitution mutation

one nucleotide is replaced by another

Deletion mutation

one or more nucleotides are removed from the gene

Insertion

one or more nucleotide are added to a gene

Missense mutation

a substitution mutation results in the wrong amino acid; responsible for Sickle cell disease

Silent mutation

a substitution mutation occurs, but the same amino acid is produced because most amino acids are coded for by more than one codon

Nonsense mutation

a substitution results in the production of a stop codon

Single Nucleotide Polymorphism

individual nucleotide difference between different people

Polymorphism

variation in DNA sequence

Frameshift mutation

insertion and deletion mutations which drastically affect proteins because they shift the reading frame and cause different sets of codons to be read

Gene Expression

the transcription and translation of a gene to make an active protein product

Constitutive expression

Gene is expressed at all times

Inducible expression

gene expression is off until actively turned on

Repressible expression

gene expression is on until actively turned off

Trans Regulatory DNA sequences

are located anywhere

Cis Regulatory DNA sequences

neat gene binding sites for transcription factors

Activators

increase transcription

Repressor

decrease transcription

Enhancer

attracts activator

Silencer

attracts repressor

Operon

multiple genes with one promoter, only exist in prokaryotes

Transcription of a gene begins with a _________ and ends with a __________.

A) promoter, terminating sequence/poly-A signal sequence

B) promoter, stop codon

C) start codon, stop codon

A) promoter, terminating sequence/poly-A signal sequence

Translation of a protein begins with a _________ and ends with a __________.

A) promoter, terminating sequence/poly-A signal sequence

B) promoter, stop codon

C) start codon, stop codon

C) start codon, stop codon

Translation of a mRNA goes in the ______ direction and the first part of the polypeptide built is the ________.

A) 3'->5';C-terminus

B) 3'->5';N-terminus

C) 5'->3';C-terminus

D) 5'->3';N-terminus

D) 5'->3';N-terminus

Transcription produces this copy of the genetic code that can then be read to make proteins

A) DNA

B) mRNA

C) tRNA

D) rRNA

E) snRNA

B) mRNA

Which of the following mutations would be the least likely to affect a protein's function?

A) nonsense mutation

B) missense mutation

C) deletion mutation

D) insertion mutation

B) missense mutation

Which of the following could cause a difference in the size of a gene's mRNA in two different samples?

A) Alternative splicing

B) A deletion mutatoin

C) A nonsense mutation

D) A and B

E) All of the above

D) A and B

Which of the following could cause a difference in the size of a gene's protein in two different samples?

A) Alternative splicing

B) A deletion mutation

C) A nonsense mutation

D) A and B

E) All of the above

E) All of the above

Which of the following is/are unique to eukaryotes?

A) Simultaneous transcription and translation of the same mRNA

B) 3' poly-a tail

C) Transcription factors

D) Both B and C

E) All of the above

B) 3’ poly-A tail

If you looked at the molecules found in different cells in the same body, you would expect them to have different...

A) DNA

B) tRNAs

C) mRNAs

D) rRNAs

E) All of the above

C) mRNAs

Which of the following statements about transcription factors is FALSE?

A) The genes for transcription factors are trans regulatory elements

B) Transcription factors can help RNA Polymerase transcribe a gene

C)Transcription factors can prevent RNA Polymerase from transcribing a gene

D) Transcription factors bind to specific sequences on the DNA called cis regulatory sequences

E) Transcription factors attach to the ribosome

E) Transcription factors attach to the ribosome

If a gene is transcribed all of the time this is an example of…

A) constitutive expression

B) inducible expression

C) repressible expression

D) none of the above

A) constitutive expression

If the lac repressor protein was absent or broken, you would expect strong expression from the lac operon...

A) all of the time

B) whenever lactose is present

C) whenever glucose is absent

D) only when lactose is present and glucose is absent

E) never

C) whenever glucose is absent

If the CAP protein was absent or broken, you would expect strong expression from the lac operon...

A) all of the time

B) whenever lactose is present

C) whenever glucose is absent

D) only when lactose is present and glucose is absent

E) never

E) never

Untranslated regions (UTRs) refer to...

A) Parts of an mRNA before the start codon and after the stop codon

B) Exons

C) DNA regions between genes

D) Codons that don't have a corresponding tRNA that can read them

A) Parts of an mRNA before the start codon and after the stop codon

You perform a mutagenesis experiment to create mutant versions of the SNELL gene from a bacterium you are studying. You end up creating a strain of your bacteria where the Snell protein has the same structure and function, but there is less of the protein produced. Which of the following mutations could explain this result?

A) A deletion mutation in the protein coding region of SNELL

B) A substitution mutation in the 5'UTR of SNELL

C) A substitution mutation in a cis regulatory element for the SNELL gene

D) B and C

E) All of the above

D) B and C

What role do double-stranded RNAs (dsRNAs) play in gene expression?

A) dsRNAs activate RNA interference (RNAi) mechanisms that suppress the expression of mRNAs that are complimentary to them

B) dsRNAs are part of the splicesome

C) dsRNAs are never found in cells

D) dsRNAs are translated to make proteins

A) dsRNAs activate RNA interference (RNAi) mechanisms that suppress the expression of mRNAs that are complimentary to them

Which of the following statements about cDNA is FALSE?

A) cDNA is complementary to mRNA

B) cDNA can be used in techniques that test for levels of gene expression

C) cDNA contains both introns and exons

D) cDNA can be made using poly-T primers

C) cDNA contains both introns and exons

cDNA prepared from cancer cells is labeled red and cDNA prepared from normal tissue is labeled green. A DNA microarray experiment is performed, and it indicates that there are high levels of expression of the gene CDK4 in the cancer cells compared to no expression in normal tissue. What result indicated this?

A) The spot corresponding to CDK4 is yellow.

B) The spot corresponding to CDK4 is red.

C) The spot corresponding to CDK4 is green.

D) The spot corresponding to CDK4 is black.

E) None of the above.

B) The spot corresponding to CDK4 is red.

You want to confirm results from the microarray in the previous question by performing a qPCR for the CDK4 cDNA from both samples. You plot the results of the qPCR on a graph with PCR cycles on the x axis and relative fluorescence on the y axis. Which of the following results would confirm the results of the microarray that expression of CDK4 is higher in the cancer cells?

A) The curve for CDK4 from the cancer cells would rise above the threshold further left on the graph than the normal tissue.

B) The curve for CDK4 from the cancer cells would rise above the threshold further right on the graph than the normal tissue.

C) The curve for CDK4 from the cancer cells would reach a higher maximum fluorescence than the normal tissue.

D) qPCR is not an appropriate technique for confirming the results of the microarray

A) The curve for CDK4 from the cancer cells would rise above the threshold further left on the graph than the normal tissue.

You decide to take it a step further and confirm that the change in mRNA levels also leads to a change in protein. Which of the following tools or techniques would be helpful in assessing the level of CDK4 protein in your samples?

A) A northern blot

B) An antibody against CDK4

C) Fluorescent in situ hybridization

D) A reporter gene attached to the CDK4 promoter

B) An antibody against CDK4